Virtual
by linda.ljc
Summary: Colonel Sheppard didn't call many people "friend", not out loud, but everyone knew where they stood with John.


**Title: Virtual**

 **Author: linda. ljc**

 **fandom: Stargate Atlantis**

10/7/16

 **Summary:** Colonel Sheppard didn't call many people "friend", not out loud, but everyone knew where they stood with John.

 **Beta:** Thanks so much Annie. It's great to have someone give it a read. I've caught so many goofs myself in various stories, things that were obvious but somehow had become invisible to my eye. Any errors left are mine.

 **Warning:** Death fic (nothing graphic). AU.

 **Spoiler:** The various characters that show up might seem inappropriate for canon, but it's intended.

 **Characters:** John Sheppard, Atlantis, many others.  
 **Category:** Drama, Angst

 **Disclaimer:** The characters and settings of Stargate SG-1 and Stargate: Atlantis belong to Showtime/Viacom, MGM/UA, Double Secret Productions, and Gekko Film Corporation. All other publicly recognizable characters, settings, etc. are the property of their respective owners. The original characters and plot are the property of the author. The author is in no way associated with the owners, creators, or producers of Stargate: SG-1 and Stargate: Atlantis or any other media franchise. No copyright infringement is intended.

 _This story was written by linda. ljc with the love of the show in mind._

 **Prologue**

John didn't tend to wake slowly, but today was different. Everything was limned in that hazy glaze of sunlight that made everything seem out of phase; or maybe like life was in slow motion. He tried a deep breath and he wasn't sure what tipped him off that maybe everything wasn't just a lazy hazy day. It might have been the slightly smoky smell or the wind whispering through trees that Atlantis didn't have, but it was probably the knife sharp pain in his abdomen. When he finally tried to straighten from the pain he noticed the dried blood from a head wound that was keeping one eye closed.

He worked that eye open and got a good look at the Jumper he was in. No wonder he could hear the wind. There was a vertical tear near the back ramp. That ramp would never close again.

John's heart rate kicked into high gear. He tried to sit upright but it was a slow process. He was terribly nauseous and very thirsty. He found the water dispenser and took only a mouthful. He really didn't want to vomit with this pain in his belly. He could tell he needed medical care, and soon. This wasn't pain that he should just work through. He needed to get to the infirmary on Atlantis.

Atlantis. The Wraith! That was the "why". The attack had been devastating. There were more hives than they'd ever seen in one place. He was in one of the last Jumpers left flying and there'd been massive damage to the piers. The central part of the city had still had a shield but power problems were proliferating. They'd held off evacuating because the Daedalus was in contact, and a Wraith hive was already heading toward it. If it could reach them, maybe they could back each other up. He had to get back.

He turned to gaze at the vertical tear and swore under his breath. Maybe it would fly in atmosphere.

Maybe it wouldn't fly at all. He worked for hours trying to jury-rig a fix, getting more desperate as the sun tracked across the sky. He'd almost given up when he managed to get the HUD to connect with him. It was able to reroute power, what there was of it, but not shields or defensive weapons or inertial dampeners, or anything else. But it would fly, which was kind of crazy, because it was the least aerodynamic creation he'd ever seen.

John thought maybe he wouldn't tease Rodney about not being able to fly in a straight line, because John wasn't doing so well today. He hoped Rodney was still alive to commiserate with about flying a Jumper that couldn't tell you what was up and what was down. He knew Rodney could appreciate the problem. If he was still alive. Be alive Rodney.

 **Denouement**

Atlantis was devastated during the last Wraith attack. It should have sunk beneath the waves. The Expedition members had fought desperately, and in the end even the self-destruct had failed them. There were no drones left to fight with, there wasn't enough power for the shield, and Wraith invaded the city. They'd seen John go down. When his signal was lost, so perhaps, was Atlantis.

John had been piloting the last surviving Jumper. He'd crashed on the mainland sustaining severe injuries and was presumed dead. He had fought through the pain but it had taken several frantic hours to repair the Jumper enough just to fly to where Atlantis rested. The fight, and the war, was already over when he finally made it back. There wasn't much left to scavenge on Atlantis, but he tried, the Jumper simply couldn't be coaxed to move again.

Atlantis barely rode above the waves with its battered and scorched facade. The reason it was still afloat was probably because the north and south piers had sheared off instead of pulling the city down. John fought his way inside through the debris. There were few bodies left to be found, and most of those were Wraith-withered husks. He really didn't want to see their faces. Mourning had to come later. If there was a later.

John knew he had to find the Chair Room. Being the center of Atlantis' defense it was the most structurally sound, but he was still surprised that it had survived. There were scorch marks and debris outside in the hall, but inside it looked untouched, like the Wraith hadn't found it. He wondered for a moment how Atlantis had protected it, but his own nearly impossible task was before him. He also knew his time was short. His injuries were infected, and the infirmary was a lost cause.

He'd seen Rodney tinker with enough Ancient devices to give him a clue where to begin. He was able to switch out crystals until something lit up, but the ZPM was so close to entropy that the Chair only flickered. Unfortunately there were things John desperately had to know, so he gave it a try.

Did the Daedalus survive? Debris now littered the system of Lantea. There weren't any pieces large enough to hold a survivor, so when no light signs were detected, not human or Wraith, he gave up on that search. There was enough debris to account for the Earth ship, but he wasn't giving up hope yet.

Had the Expedition managed to evacuate at least some of them through the Gate? If some had escaped this destruction he had to believe that there was still hope for Pegasus and Earth. He poured over the details of the battle's last moments. He found what he needed to know and it was overwhelming. Some of Caldwell's people had beamed to the city before the ship was destroyed, but the Wraith kept a wormhole open during their attack. Atlantis' had blocked an incursion through the incoming wormhole with the iris, but it had kept any survivors from escaping.

Atlantis showed him their last moments. Rodney's last efforts were there for him to see. The self-destruct was set, and when it failed, there were explosions in the Gate Room. That was probably Cadman's work. Rodney had set a virus loose that he had developed "just in case". It sought out all references to Earth and the Milky Way and burned them from Atlantis' memory. During the last moments the crystal that made travel to Earth possible was removed. John could only hope that Rodney, or someone, had been able to destroy it. And now, what was left, was what he could see. So, no one escaped, no one survived, except him.

Now he knew there wasn't any hope. There was really nothing else he could do. There was no foe here left to fight. There was no one left to stand with. Where could he go? How would he get there? He couldn't even get out a message to warn Earth.

 **"To sleep, perchance to dream.."**

His radio beeped a signal. "Sheppard here."

Elizabeth answered. "John, are you just coming back from your walk?"

"Jog, Elizabeth. Jog."

"Oh, excuse me. Is that what you call it these days?"

"Yeah, yeah. I know. Ronon will make sure I'm running soon. Do you need something?"

"Just meet me for lunch?"

"Well, I have some paperwork that probably has to have been done yesterday, but … you talked me into it."

"Good. Maybe Sam and Mr. Woolsey can join us today."

"That's good. But not Everett?"

"Not Everett, John. He's not here, not today."

"I'll call McKay and see if he's busy."

"Rodney's always busy, but please try to tear him away from his lab for a while. For today, whatever he's working on can wait."

When he reached the lab he stopped just inside the door. He watched his long-time teammate, Rodney McKay, bicker with Radek. It sounded like he was just in time to prevent their academic squabble from coming to blows. He'd bet on Rodney if it came to that. "Haven't you two figured that out yet?"

"Of course I have."

Radek got right up to Rodney and spluttered, "Except for that little fraction of the speed of light, you mean."

"Open your eyes! It's accounted for it in this inverse ..."

Sheppard tilted his head as he perused the whiteboard and it's hieroglyphic equations and added, "You're sure that will take care of the whole deviation?"

Rodney whipped around, "Yes, I'm sure." He crossed his arms and tapped his foot.

John laughed. "You look like my old grandmother, Rodney."

Rodney squawked his displeasure.

"Now you really do. Come on. It's lunch time." John thought he might have overdone the comparison a bit so he smiled and added, "You'd have liked Grams. She was great."

Rodney's pique ebbed a bit and he reluctantly closed his laptop. "No tava beans."

"I'll save you from the tava beans."

"Good. Because I hate tava beans."

"I know." John just rolled his eyes and thought, Everyone knows.

They chatted as they walked to the door. John turned and asked, "Aren't you coming Radek? Miko, I'd love to have you and Simpson join us, too."

They nodded to each other, smiled, and turned away from their computers as if they had suddenly become radioactive. They all chatted happily as they headed to the mess hall.

As they reached the mess hall door, John heard light footsteps that seemed to hurry toward him.

"Colonel Sheppard. Could I have a minute?"

"Doctor Keller. Is there something I can do for you?"

"Well, I was just wondering if the traveling clinic will be rescheduled for next week. If we get too far off schedule we'll have to work out something for the timing of vaccinations."

John hadn't noticed Carson until the doctor chimed in with a word of agreement.

Carson said, "If it isn't possible I could send out a couple of our Physician Assistants. They can let us know if anything urgent has presented itself, and they can handle the vaccinations easily, but they'll need military escorts."

John thought for a moment. "We'll discuss it in tomorrow's briefing, but it sounds like a good option if you both agree."

Keller nodded when Carson smiled his agreement.

Carson glanced aside and noticed another arrival. "Well, here's Dr. Biro as well. We might as well have lunch since we're here. It looks like there's going to be quite a crowd, John."

Evan Lorne had just left the transporter for the mess hall with Parish. They were talking animatedly about something. They seemed as odd a pair as John and Rodney, yet they'd become close. Lorne gave John a friendly nod as they passed through the door to the mess. Lorne said, "I hear it's going to be something special today."

A sudden lurch from Atlantis had John's immediate attention. "McKay. What was that?"

There was a catch in John's breath as he glanced around. It felt a little like the disorientation he felt when he stepped out on a new planet, not knowing what to expect. He'd get one glance to gather in his surroundings like a movie stop-action scene. That one glance had to tell him everything. But here, everyone around him had stopped moving with that lurch … and then everything started again like nothing had happened.

"Rodney. Tell me what happened!"

And Rodney McKay, who could turn on a dime from confident to panicked looked so serene that it only added to the surreal moment.

"It was nothing, John. If you're worried I can put Kavanagh on it. He's on duty now."

"Kavanagh? Really?"

"It's really nothing for you to worry about. You'll see. Even Kavanagh can handle it."

"Well … alright … if you're sure." John believed Rodney. He did. It was just that it felt wrong in some way that he couldn't define. Everyone must have just been surprised like he was.

Just at that moment Elizabeth came through the mess hall door and spotted John. "There you are. We've been waiting for you." With a glance at Rodney she added, "Hurry up before the tava beans are all gone."

John knew the last bit was to tease McKay.

"John's having mine. Come on Sheppard. I hope you're hungry. And everything is fine. Everyone's here or on their way."

Suddenly Lieutenant Ford came jogging up the hallway yelling, "Hey! Wait for me." He had just reached the transporter entrance as the door slid open again.

As Ronon stepped out he clapped the young man on the shoulder, knocking him forward another step. "Hey, Ford. Good to see you." Then he turned back toward the transporter as he said, "Sheppard. Look who came back early." Coming through the door were Teyla and Torren with Halling and Jinto.

Teyla smiled around Torren's waving hand. "We would not miss this, John. Have you seen Keras yet? He's back for a visit, too."

"I haven't seen him yet, but I'm glad all of you could make it."

John walked slowly to the table surrounded by his teammates. He relaxed even more as he greeted more Expedition members that were already seated. Bates. Markham. Griffin. Doctors Grodin. Gaul, and Abrams.

John turned to Rodney and said, "I think it's going to be a full house today."

"Good day to you, Colonel Sheppard."

John was amazed. "Captain Helia."

Helia glanced at some of the crew that had accompanied her. "We were told that we should come today, that it was … something special."

"I'm glad you … and some of your crew could be here. This was your home. We want you to always feel welcome."

When he looked again the table seemed to have lengthened and almost disappeared in the distance with more old friends coming to join them, greeting him with, "John," "Colonel," "Sheppard," "Good morning, Sir,". All his Lantean friends, military and civilian, from Earth, from Athos and elsewhere in Pegasus, were there to have lunch with him. Friendly chatter filled the air as he looked about him. It felt like old times. Like home should feel.

He sat down to a tray already filled with some of his favorite things. It had been a while since his last turkey sandwich. The

supplies the Daedalus brought were really appreciated by those that longed for simple reminders of Earth. In among those offerings were Pegasus items like the tava beans and fresh fruit. Everyone had trays filled with their favorites, too. Favorite things. Old friends.

Wait. There was something he was forgetting about Ford, wasn't there? Something from long ago. He couldn't seem to remember. Oh well, maybe Sumner would know. He'd have to ask him when he saw him again.

Another lurch, smaller than the first. No one seemed to notice this time except John. Well, Rodney had, and he once again said not to worry, but as he looked around, the scene seemed surreal. Perhaps déjà vu described it. Everything was as it once was, but wasn't. Did that even make sense?

"Rodney?"

"Everything is fine, John. See, Kavanagh has already made progress. Remember, we're all here for you. We just want you to enjoy yourself."

John looked around, at all the smiling faces turned to him. John could only smile back. This was a good day. The day was one he would remember always. The best. But even so, there was an unease he didn't want to acknowledge, perhaps because he knew there would be an end, because there always was.

He was sorry when the end came. When the walls of the mess slowly faded to gray. When details dropped away. When conversations became an indistinct murmur. And then the floor seemed suddenly insubstantial leaving him with the floaty feeling he got from the really good drugs.

He tried to hold on to his memories as everything seemed to waver in and out of focus. He felt a little light-headed and everything blurred. He rubbed at his eyes as the room slowly darkened. He looked around him as the chatter faded completely away. Suddenly he felt very tired. More tired than was really called for after his morning walk and a meal with friends.

Somehow he wasn't surprised to see Rodney standing at his side. "Where is everyone, Rodney?"

"We're here with you, John, don't worry. You've been in the Control Chair a long time. Maybe your body is telling you to get some rest."

John felt confused. "I'm in the Chair? I was just having lunch with ..."

"I know. You wanted to see all of us one more time before … before your rest."

John smiled for a moment. "It was good to see everyone. We should do that more often."

"Yes. It was good to be with friends. Atlantis has always felt like home."

 **Epitaph**

Atlantis' ocean was calm as glass this last day. Smoke still hung like a shroud to hide the most devastated areas. The city was grieving the last descendants she would know. The people who had come, who had stayed, who had fought and were ready to destroy it all, even to the last man and woman, to prevent the Wraith from winning this last, terrible battle.

The only hope was the fact that Daedalus would now never reach Earth. It would be the only warning it's people would receive. She hoped they recognized it for what it was. If they did, they might some day know the fate of her … their … Expedition.

They would know the fate of Atlantis. They would know they did not surrender. They would know and be proud of these descendants who were so few. That stood against an enemy that was so hungry. She would hold this hope that they would be remembered.

There was no one left to stand with, there was no place to go, and no way to get there. John Sheppard was right in his last assessment except for one thing.

"Atlantis? Are you … awake?"

"I am here."

"I'm sorry, Atlantis."

"Do not be sorry, John Sheppard. I rejoiced when I awoke to your arrival with your Expedition. I do not regret your coming; only that our time is done."

The lights flickered faintly and went out.

John's heart skipped a beat in fear. "Atlantis? I want you to know. They'll fight. Earth will fight."

"I believe you, John Sheppard. We can go to our rest knowing this is true."

"Thank you, Atlantis."

"Thank you, John Sheppard."

Only a bare whisper of the city's once tremendous power had been left after the devastation of the attack. It had barely been enough to keep it above the calm waves. With the last of her power she sealed the Chair Room, then lowered the last boundaries between herself and the sea. Slowly she settled, as gently as she could. Her only goal now was to settle it whole, not shattered. There might still be visitors some day when the AI was no more. It would be something to hope for in her last moments as she allowed the memory of Earth to slip away.

Now the city was barren of life once again. The war was lost, or at least this battle for Atlantis. The fight would now pass to other hands. Now that John Sheppard had said his final goodbyes the city's last purpose had been fulfilled and Atlantis had slipped beneath the waves. The City of the Ancients was finally at rest with only the Lantean whales to mourn it's passing.

finis


End file.
